[Freesurfer] A question on fsaverage

[peng]

Hi everyone,

   I am a new user of freesurfer. As a first step, I wrote a script (see
below between ---) to run recon-all on the anatomical data. Since I found
it very slow, and our server has multi-cores, I run this script manually
several times, thus it appeared to be parallel.Then I have several
questions:

1 From the screen output, I guess if a certain subject folder exists,
freesurfer will refuse to work on this subject. Then I have assumption that
if I run the same script multiple times would not overwrite results from
previous session. Can I hold this believe?
2 After certain time, I found new folders with name such as [fsaverage],
which I assumed as kind of average of subjects. Then I worry this was
generated from one  session (either the first one or the last one,
depending on overwriting policy of this folder). For example, if session
one worked on subject 1 4 7 ... and session two worked on subject 2 5 8...
and session three worked on subject 3 6 9 ... ; is this [fsaverage] an
average of (subject 1, 4, 7) or  (subject 3, 6, 9)? Or I am so lucky that
it is the average all processed subjects?
3 Is there a proper way to work in parallel than my stone-age way?
4 I searched the wiki and found some slides and pages which may help but
not answering the above question. Would you please suggest an example
"full" script of analysis?
Thank you very much!
===
My environment: 64-bit Linux with OpenSUSE. 8-CPUs/32G mem
Script:
-
#!/bin/csh
echo "beginning ..."

#environment setup
source ~/1tests/FreeSurferEnv.csh

#Set environment and get the filelist
set raw_dir = '~/2rawdata/'
set fileNameList = `ls {$raw_dir}`

#Try all the subjects in a loop
foreach file ($fileNameList)
echo "Now processing file ($file): ..."
echo ""
set inName = ($raw_dir$file)
recon-all -i $inName -s $file -autorecon-all
end

echo "done!"
-
===
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[Freesurfer] Fwd: A question on fsaverage

[peng]

Hi everyone,

   I just re-checked the folder [fsaverage], their modified date was quite
old, probably they are just copies from freesurfer installation folder
rather than results of my scripts. Then my question 2 become void...

best!
Peng

-- Forwarded message --
From: peng 
Date: Thu, Feb 6, 2014 at 11:00 AM
Subject: A question on fsaverage
To: Freesurfer@nmr.mgh.harvard.edu


Hi everyone,

   I am a new user of freesurfer. As a first step, I wrote a script (see
below between ---) to run recon-all on the anatomical data. Since I found
it very slow, and our server has multi-cores, I run this script manually
several times, thus it appeared to be parallel.Then I have several
questions:

1 From the screen output, I guess if a certain subject folder exists,
freesurfer will refuse to work on this subject. Then I have assumption that
if I run the same script multiple times would not overwrite results from
previous session. Can I hold this believe?
2 After certain time, I found new folders with name such as [fsaverage],
which I assumed as kind of average of subjects. Then I worry this was
generated from one  session (either the first one or the last one,
depending on overwriting policy of this folder). For example, if session
one worked on subject 1 4 7 ... and session two worked on subject 2 5 8...
and session three worked on subject 3 6 9 ... ; is this [fsaverage] an
average of (subject 1, 4, 7) or  (subject 3, 6, 9)? Or I am so lucky that
it is the average all processed subjects?
3 Is there a proper way to work in parallel than my stone-age way?
4 I searched the wiki and found some slides and pages which may help but
not answering the above question. Would you please suggest an example
"full" script of analysis?
Thank you very much!
===
My environment: 64-bit Linux with OpenSUSE. 8-CPUs/32G mem
Script:
-
#!/bin/csh
echo "beginning ..."

#environment setup
source ~/1tests/FreeSurferEnv.csh

#Set environment and get the filelist
set raw_dir = '~/2rawdata/'
set fileNameList = `ls {$raw_dir}`

#Try all the subjects in a loop
foreach file ($fileNameList)
echo "Now processing file ($file): ..."
echo ""
 set inName = ($raw_dir$file)
recon-all -i $inName -s $file -autorecon-all
end

echo "done!"
-
===
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Re: [Freesurfer] A question on fsaverage

[peng]

Bruce, Thanks a lot!
Would you explain more on how to run recon-all in parallel? By run the
script it did not automatically took the advantage of multiple cores (by
checking CPU usage). Is their somewhere I can change the preference or I
shall add some parameters in my code?


On Thu, Feb 6, 2014 at 2:39 PM, Bruce Fischl wrote:

> Hi Peng
>
> the recon-all instances should be able to be run in parallel. The first
> time you run one it will see that fsaverage does not exist, and will
> symlink it to $FREESURFER_HOME/subjects/fsaverage (which is our existing
> coordinate system, NOT an average of your subjects - to make your own
> average use the make_average_subject script).
>
> cheers
> Bruce
>
>
>
>  On Thu, 6 Feb 2014, peng wrote:
>
>  Hi everyone,
>>
>>I am a new user of freesurfer. As a first step, I wrote a script (see
>> below between ---) to run recon-all on the anatomical data. Since I found
>> it
>> very slow, and our server has multi-cores, I run this script manually
>> several times, thus it appeared to be parallel.Then I have several
>> questions:
>>
>> 1 From the screen output, I guess if a certain subject folder exists,
>> freesurfer will refuse to work on this subject. Then I have assumption
>> that
>> if I run the same script multiple times would not overwrite results from
>> previous session. Can I hold this believe?
>> 2 After certain time, I found new folders with name such as [fsaverage],
>> which I assumed as kind of average of subjects. Then I worry this was
>> generated from one  session (either the first one or the last one,
>> depending
>> on overwriting policy of this folder). For example, if session one worked
>> on
>> subject 1 4 7 ... and session two worked on subject 2 5 8... and session
>> three worked on subject 3 6 9 ... ; is this [fsaverage] an average of
>> (subject 1, 4, 7) or  (subject 3, 6, 9)? Or I am so lucky that it is the
>> average all processed subjects?
>> 3 Is there a proper way to work in parallel than my stone-age way?
>> 4 I searched the wiki and found some slides and pages which may help but
>> not
>> answering the above question. Would you please suggest an example "full"
>> script of analysis?
>> Thank you very much!
>> ===
>> My environment: 64-bit Linux with OpenSUSE. 8-CPUs/32G mem
>> Script:
>> -
>> #!/bin/csh
>> echo "beginning ..."
>>
>> #environment setup
>> source ~/1tests/FreeSurferEnv.csh
>>
>> #Set environment and get the filelist
>> set raw_dir = '~/2rawdata/'
>> set fileNameList = `ls {$raw_dir}`
>>
>> #Try all the subjects in a loop
>> foreach file ($fileNameList)
>> echo "Now processing file ($file): ..."
>> echo ""
>> set inName = ($raw_dir$file)
>> recon-all -i $inName -s $file -autorecon-all
>> end
>>
>> echo "done!"
>> -
>> ===
>>
>>
>>
>>
>>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
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[Freesurfer] distribute dots on the surface

[peng]

Dear Freesurfers,

   I have run recon-all and got a set of surfaces for the subjects. I wish
to distribute N dots about evenly on the surface to cover most gyri and
sulci , but I don't how to implement that. One way is to manually put them
in the GUI of freeview, but it is not so convenient if N is relative large
(say, 200). Can anyone give me a hint which function shall I use?


best
Peng
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Re: [Freesurfer] distribute dots on the surface

[peng]

Thanks，I will try。


On Thu, Feb 13, 2014 at 9:47 PM, Douglas N Greve
wrote:

>
> Please remember to post the list and not to us personally. Thanks!
> Actually, I don't know of a good way to do what you want to do (I thought I
> had an idea, but it won't work). One way to do this would be to select a
> random set of vertices. This would be approximately uniform. Alternatively,
> you can use mris_make_face_parcellation but you will be limited by the
> icosahedral series. If you want to go with the first option, you can run
>
> mri_volsynth --temp subject/surf/lh.thickness --pdf uniform --o junk.mgh
>
> mri_binarize --i junk.mgh --min .9 --o mask.mgh
>
> The first command synthesizes a surface overlay with uniformly distributed
> random numbers between 0 and 1. The second command thresholds at .9, so
> you'd get about 10% of the vertices
>
> doug
>
>
>
>
>
> On 02/13/2014 02:20 AM, peng wrote:
>
>> Hi Douglas,
>>
>>Thanks for your reply. Yes, I mean "a mask surface overlay with 1s in
>> some vertices and 0s in others". And I also wish to convert there
>> coordinates back to the volume coordinates later (e.g. RAS etc.), which I
>> think is possible.
>>
>>
>> On Wed, Feb 12, 2014 at 4:15 PM, Douglas Greve 
>> > gr...@nmr.mgh.harvard.edu>> wrote:
>>
>>
>> what do you mean by "dots"? Eg, a mask surface overlay with 1s in
>> some vertices and 0s in others? Or a label?
>> doug
>>
>>
>>
>>
>> On 2/12/14 9:52 AM, peng wrote:
>>
>>> Dear Freesurfers,
>>>
>>>I have run recon-all and got a set of surfaces for the
>>> subjects. I wish to distribute N dots about evenly on the surface
>>> to cover most gyri and sulci , but I don't how to implement that.
>>> One way is to manually put them in the GUI of freeview, but it is
>>> not so convenient if N is relative large (say, 200). Can anyone
>>> give me a hint which function shall I use?
>>>
>>>
>>> best
>>> Peng
>>>
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu  <mailto:freesur...@nmr.mgh.
>>> harvard.edu>
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu
>> >
>>
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> The information in this e-mail is intended only for the person to
>> whom it is
>> addressed. If you believe this e-mail was sent to you in error and
>> the e-mail
>> contains patient information, please contact the Partners
>> Compliance HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to
>> you in error
>> but does not contain patient information, please contact the
>> sender and properly
>> dispose of the e-mail.
>>
>>
>>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
>
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[Freesurfer] project locations from template to individual MRIs

[peng]

Dear freesurfers,

   I have a set of dot locations (300~400) in a template brain, indicated
by indices of a 3-D array of the template MRI data, which can be easily
transformed to RAS coordinates. I wish to project these dot locations to
individual MRIs, ideally also as indicated by indices in the 3-D array of
the individual MRI data. Is it possible to do it in freesurfer? I guess the
surface-based procedure shall work well for this. It might be a very junior
question, if it was documented somewhere before, please let me know the
link. Thank you very much for help.

best
Peng
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Re: [Freesurfer] project locations from template to individual MRIs

[peng]

Thanks Doug for your reply. In fact I need both. I do this mainly for
computation (in volume); and display (in surface) is also cool.

The dots (e.g. A1, A2, ..., An, ..., AN) were originally defined in volume
of the template (icbm152). This can be implemented as an Nx3 matrix S,
where S(n, :) = [nx, ny, nz] indicates the location of An in the volume.
RAS here I mean such a coordinate system that, [0 0 0] is AC and the 3
dimensions are taking right, anterior, superior as positive, e.g An([nx0
ny0 nz0]) indicates a location nx0 mm right, ny0 mm anterior and nz0 mm
superior of AC.
The above two systems can be easily transformed by a transformation matrix.

I wish to know the correspondent locations of An in individual subject(B),
as Bn. e.g. if A1 is center of V1 in the template, I wish to find the
center of V1 in the subject as B1.
So far, all the locations are represented in volume. However, I guess to
normalise the individual brain to the template, freesurfer will extract the
volumes to surfaces. I imagine the procedure will be like An (volume
representation of dots in template)  -> ASn (surface representation of dots
in template) -> BSn(surface representation of dots in individual) ->
Bn(volume representation of dots in individual). If this assumption is
correct, I would like to use Bn for my computation and ASn for display
later.

I hope I have made myself clearer.

best
Peng


On Mon, Mar 10, 2014 at 4:21 PM, Douglas N Greve
wrote:

>
> Do you mean you want to display them in the MRI volume or on the surface
> (or both)? When you say that they are in "RAS coordinates", what do you
> mean? How are the coords defined?
> doug
>
>
>
> On 03/08/2014 07:26 AM, peng wrote:
> > Dear freesurfers,
> >
> >I have a set of dot locations (300~400) in a template brain,
> > indicated by indices of a 3-D array of the template MRI data, which
> > can be easily transformed to RAS coordinates. I wish to project these
> > dot locations to individual MRIs, ideally also as indicated by indices
> > in the 3-D array of the individual MRI data. Is it possible to do it
> > in freesurfer? I guess the surface-based procedure shall work well for
> > this. It might be a very junior question, if it was documented
> > somewhere before, please let me know the link. Thank you very much for
> > help.
> >
> > best
> > Peng
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
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Re: [Freesurfer] project locations from template to individual MRIs

[peng]

Thanks for your reply. I am using *ICBM 2009a Nonlinear Asymmetric 1×1x1mm
template. *I did not expect that it will make much difference in the
algorithm. Does freesurfer favor certain template than others?
btw: the individual mri is also 1 mm resolution.


On Tue, Mar 11, 2014 at 8:46 PM, peng  wrote:

> Thanks for your reply. I am using *ICBM 2009a Nonlinear Asymmetric
> 1×1x1mm template. *I did not expect that it will make much difference in
> the algorithm. Does freesurfer favor certain template than others?
> btw: the individual mri is also 1 mm resolution.
>
>
> On Tue, Mar 11, 2014 at 5:59 PM, Douglas N Greve <
> gr...@nmr.mgh.harvard.edu> wrote:
>
>>
>> what template? When discussing coordinate systems you have to be very
>> specific. A template could be a volume template or a surface template. If a
>> volume template it could be MNI305 or MNI152. If MNI152 it could be the 1mm
>> version or the 2mm version. All of these things are important and the
>> questions cannot be answered without these details.
>> doug
>>
>>
>>
>>
>>
>> On 03/11/2014 12:42 PM, peng wrote:
>>
>>> Thanks Doug, I will read the document. But may I ask a simpler question:
>>> in freesurfer, do you use affine transformation to make correspondence
>>> between a individual subject and the template (the procedure someone calls
>>> as normalization)?
>>>
>>> best
>>> Peng
>>>
>>>
>>> On Tue, Mar 11, 2014 at 5:06 PM, Douglas N Greve <
>>> gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>>>
>>>
>>> Hi Peng, there's a lot going on there, and it is not specific
>>> enough for
>>> me to make recommendations. Take a look at the docs we have on our
>>> coordinate systems
>>>
>>> http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems?
>>> action=AttachFile&do=get&target=fscoordinates.pdf
>>>
>>> you might get the answer you need from there or at least use our
>>> terminology to point me in the right direction
>>>
>>> doug
>>>
>>>
>>>
>>>
>>> On 03/10/2014 12:20 PM, peng wrote:
>>> > Thanks Doug for your reply. In fact I need both. I do this
>>> mainly for
>>> > computation (in volume); and display (in surface) is also cool.
>>> >
>>> > The dots (e.g. A1, A2, ..., An, ..., AN) were originally defined in
>>> > volume of the template (icbm152). This can be implemented as an Nx3
>>> > matrix S, where S(n, :) = [nx, ny, nz] indicates the location of
>>> An in
>>> > the volume.
>>> > RAS here I mean such a coordinate system that, [0 0 0] is AC and
>>> the 3
>>> > dimensions are taking right, anterior, superior as positive, e.g
>>> > An([nx0 ny0 nz0]) indicates a location nx0 mm right, ny0 mm
>>> anterior
>>> > and nz0 mm superior of AC.
>>> > The above two systems can be easily transformed by a transformation
>>> > matrix.
>>> >
>>> > I wish to know the correspondent locations of An in individual
>>> > subject(B), as Bn. e.g. if A1 is center of V1 in the template, I
>>> wish
>>> > to find the center of V1 in the subject as B1.
>>> > So far, all the locations are represented in volume. However, I
>>> guess
>>> > to normalise the individual brain to the template, freesurfer will
>>> > extract the volumes to surfaces. I imagine the procedure will be
>>> like
>>> > An (volume representation of dots in template)  -> ASn (surface
>>> > representation of dots in template) -> BSn(surface representation
>>> of
>>> > dots in individual) -> Bn(volume representation of dots in
>>> > individual). If this assumption is correct, I would like to use
>>> Bn for
>>> > my computation and ASn for display later.
>>> >
>>> > I hope I have made myself clearer.
>>> >
>>> > best
>>> > Peng
>>> >
>>> >
>>> > On Mon, Mar 10, 2014 at 4:21 PM, Douglas N Greve
>>> > mailto:gr...@nmr.mgh.harvard.edu>
>>>  <mailto:gr...@nmr.mgh.harvard.edu
>>>
>>> <mailto:gr...@nmr.mgh.harvard.edu>>> wrote:
>>> 

Re: [Freesurfer] project locations from template to individual MRIs

[peng]

Hi Doug,
   With the terminology in the document you provided, I can summarize what
I want to do exactly as part of the flow chart in page 7. I listed it as
between==. As described in the document, I can get Ta, Tb by ; and R from a file ; am I right?
 Practically, I may put my template as a subject a0, and individuals as
subjects a1, a2 ..., an. What is the file name of [Vol A TkReg "RAS"] under
the subject folder?
==
   [Volume A CRS] -> (Ta) -> [Vol A TkReg "RAS"] <- (R) <- [ Vol B TkReg
"RAS"] <- (Tb) <- [Volume B CRS]
==
Thanks a lot.


On Tue, Mar 11, 2014 at 5:06 PM, Douglas N Greve
wrote:

>
> Hi Peng, there's a lot going on there, and it is not specific enough for
> me to make recommendations. Take a look at the docs we have on our
> coordinate systems
>
>
> http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems?action=AttachFile&do=get&target=fscoordinates.pdf
>
> you might get the answer you need from there or at least use our
> terminology to point me in the right direction
>
> doug
>
>
>
>
> On 03/10/2014 12:20 PM, peng wrote:
> > Thanks Doug for your reply. In fact I need both. I do this mainly for
> > computation (in volume); and display (in surface) is also cool.
> >
> > The dots (e.g. A1, A2, ..., An, ..., AN) were originally defined in
> > volume of the template (icbm152). This can be implemented as an Nx3
> > matrix S, where S(n, :) = [nx, ny, nz] indicates the location of An in
> > the volume.
> > RAS here I mean such a coordinate system that, [0 0 0] is AC and the 3
> > dimensions are taking right, anterior, superior as positive, e.g
> > An([nx0 ny0 nz0]) indicates a location nx0 mm right, ny0 mm anterior
> > and nz0 mm superior of AC.
> > The above two systems can be easily transformed by a transformation
> > matrix.
> >
> > I wish to know the correspondent locations of An in individual
> > subject(B), as Bn. e.g. if A1 is center of V1 in the template, I wish
> > to find the center of V1 in the subject as B1.
> > So far, all the locations are represented in volume. However, I guess
> > to normalise the individual brain to the template, freesurfer will
> > extract the volumes to surfaces. I imagine the procedure will be like
> > An (volume representation of dots in template)  -> ASn (surface
> > representation of dots in template) -> BSn(surface representation of
> > dots in individual) -> Bn(volume representation of dots in
> > individual). If this assumption is correct, I would like to use Bn for
> > my computation and ASn for display later.
> >
> > I hope I have made myself clearer.
> >
> > best
> > Peng
> >
> >
> > On Mon, Mar 10, 2014 at 4:21 PM, Douglas N Greve
> > mailto:gr...@nmr.mgh.harvard.edu>> wrote:
> >
> >
> > Do you mean you want to display them in the MRI volume or on the
> > surface
> > (or both)? When you say that they are in "RAS coordinates", what
> > do you
> > mean? How are the coords defined?
> > doug
> >
> >
> >
> > On 03/08/2014 07:26 AM, peng wrote:
> > > Dear freesurfers,
> > >
> > >I have a set of dot locations (300~400) in a template brain,
> > > indicated by indices of a 3-D array of the template MRI data, which
> > > can be easily transformed to RAS coordinates. I wish to project
> > these
> >     > dot locations to individual MRIs, ideally also as indicated by
> > indices
> > > in the 3-D array of the individual MRI data. Is it possible to do
> it
> > > in freesurfer? I guess the surface-based procedure shall work
> > well for
> > > this. It might be a very junior question, if it was documented
> > > somewhere before, please let me know the link. Thank you very
> > much for
> > > help.
> > >
> > > best
> > > Peng
> > >
> > >
> > > ___
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> > <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> > --
> > Douglas N. Greve, Ph.D.
> > MGH-NMR Center
> > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
> > Phone Number: 617-724-2358
> > Fax: 617-726-7422
> >
> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> >

[Freesurfer] a question on flat surface

[peng]

Hi Freesurfers,

   I have tried to obtain a flat surface as described by the upper part
(full cortex) of the following page:

   http://freesurfer.net/fswiki/FreeSurferOccipitalFlattenedPatch

   However, I failed to load the results in freeview (it took forever), nor
can I read in matlab with read_surf. The error in matlab is as following
==
Error using reshape
To RESHAPE the number of elements must not change.

Error in read_surf (line 77)
vertex_coords = reshape(vertex_coords, 3, vnum)' ;
==
   Thus I suspect in the newly generated surface, the number of vertices in
the header does not meet that indicated by the data. I did sth wrong.

Questions:
1 Is this webpage still up-to-date or I shall try something new to flatten
the surface?
2 Probably there are "frequently made mistakes" during my manual process,
would you please give me a hint? I my case afterwards mris_flatten took 2-3
hours.

btw: the inflated surface is OK either checked by freeview or matlab.

best
Peng
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[Freesurfer] Fwd: a question on flat surface

[peng]

More information, error from tksurfer is as following:


MRISalloc(16711682, 480): could not allocate vertices
Cannot allocate memory



-- Forwarded message --
From: peng 
Date: Fri, May 9, 2014 at 1:01 PM
Subject: a question on flat surface
To: "Freesurfer@nmr.mgh.harvard.edu" 


Hi Freesurfers,

   I have tried to obtain a flat surface as described by the upper part
(full cortex) of the following page:

   http://freesurfer.net/fswiki/FreeSurferOccipitalFlattenedPatch

   However, I failed to load the results in freeview (it took forever), nor
can I read in matlab with read_surf. The error in matlab is as following
==
Error using reshape
To RESHAPE the number of elements must not change.

Error in read_surf (line 77)
vertex_coords = reshape(vertex_coords, 3, vnum)' ;
==
   Thus I suspect in the newly generated surface, the number of vertices in
the header does not meet that indicated by the data. I did sth wrong.

Questions:
1 Is this webpage still up-to-date or I shall try something new to flatten
the surface?
2 Probably there are "frequently made mistakes" during my manual process,
would you please give me a hint? I my case afterwards mris_flatten took 2-3
hours.

btw: the inflated surface is OK either checked by freeview or matlab.

best
Peng
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Re: [Freesurfer] Fwd: a question on flat surface

[peng]

Thank you Bruce. I can load it as patch as you suggested. I can also load
the curvatures to color it. Thus I imagine in the data, there would be 2D
locations of the vertices, and their indices respect to the full surface.
Is it true? How can I read this information (e.g. into matlab) ?
Thanks again! Also thanks to anyone who would like to comment!

best
Peng


On Fri, May 9, 2014 at 5:12 PM, Bruce Fischl wrote:

> Hi Peng
>
> the flat maps are stored in a different format than the surfaces, called a
> "patch" format (since they are only a piece of the whole surface - not the
> entire thing). You can load them with file->load patch in tksurfer. Not
> sure about freeview, perhaps Ruopeng can comment?
>
> cheers
> Bruce
>
>
> On Fri, 9 May 2014, peng wrote:
>
>
>> More information, error from tksurfer is as following:
>>
>> 
>> MRISalloc(16711682, 480): could not allocate vertices
>> Cannot allocate memory
>> 
>>
>>
>> -- Forwarded message --
>>
>> From: peng 
>> Date: Fri, May 9, 2014 at 1:01 PM
>> Subject: a question on flat surface
>> To: "Freesurfer@nmr.mgh.harvard.edu" 
>>
>>
>> Hi Freesurfers,
>>I have tried to obtain a flat surface as described by the upper part
>> (full cortex) of the following page:
>>
>>http://freesurfer.net/fswiki/FreeSurferOccipitalFlattenedPatch
>>
>>However, I failed to load the results in freeview (it took forever),
>> nor
>> can I read in matlab with read_surf. The error in matlab is as following
>> ==
>> Error using reshape
>> To RESHAPE the number of elements must not change.
>>
>> Error in read_surf (line 77)
>> vertex_coords = reshape(vertex_coords, 3, vnum)' ;
>> ==
>>Thus I suspect in the newly generated surface, the number of vertices
>> in
>> the header does not meet that indicated by the data. I did sth wrong.
>>
>> Questions:
>> 1 Is this webpage still up-to-date or I shall try something new to flatten
>> the surface?
>> 2 Probably there are "frequently made mistakes" during my manual process,
>> would you please give me a hint? I my case afterwards mris_flatten took
>> 2-3
>> hours.
>>
>> btw: the inflated surface is OK either checked by freeview or matlab.
>>
>> best
>> Peng
>>
>>
>>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
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Re: [Freesurfer] Fwd: a question on flat surface

[peng]

Great, Thank you Bruce!


On Sat, May 10, 2014 at 3:09 PM, Bruce Fischl wrote:

> Hi Peng
>
> we provide matlab code (read_patch.m) for reading patches and for reading
> patches converted to ascii format (read_patch_asc.m). You can use
> mri_convert to generate the ascii format
>
> cheers
> Bruce
>  On Sat, 10 May 2014, peng wrote:
>
>  Thank you Bruce. I can load it as patch as you suggested. I can also load
>> the curvatures to
>> color it. Thus I imagine in the data, there would be 2D locations of the
>> vertices, and their
>> indices respect to the full surface. Is it true? How can I read this
>> information (e.g. into
>> matlab) ?  Thanks again! Also thanks to anyone who would like to comment!
>> best
>> Peng
>>
>>
>> On Fri, May 9, 2014 at 5:12 PM, Bruce Fischl 
>> wrote:
>>   Hi Peng
>>
>>   the flat maps are stored in a different format than the surfaces,
>> called a
>>   "patch" format (since they are only a piece of the whole surface -
>> not the
>>   entire thing). You can load them with file->load patch in tksurfer.
>> Not sure
>>   about freeview, perhaps Ruopeng can comment?
>>
>>   cheers
>>   Bruce
>>
>>
>>   On Fri, 9 May 2014, peng wrote:
>>
>>
>> More information, error from tksurfer is as following:
>>
>> ====
>> MRISalloc(16711682, 480): could not allocate vertices
>> Cannot allocate memory
>> 
>>
>>
>> -- Forwarded message --
>>
>> From: peng 
>> Date: Fri, May 9, 2014 at 1:01 PM
>> Subject: a question on flat surface
>> To: "Freesurfer@nmr.mgh.harvard.edu"
>> 
>>
>>
>> Hi Freesurfers,
>>I have tried to obtain a flat surface as described by the
>> upper
>> part
>> (full cortex) of the following page:
>>
>>http://freesurfer.net/fswiki/
>> FreeSurferOccipitalFlattenedPatch
>>
>>However, I failed to load the results in freeview (it took
>> forever), nor
>> can I read in matlab with read_surf. The error in matlab is as
>> following
>> ==
>> Error using reshape
>> To RESHAPE the number of elements must not change.
>>
>> Error in read_surf (line 77)
>> vertex_coords = reshape(vertex_coords, 3, vnum)' ;
>> ==
>>Thus I suspect in the newly generated surface, the number
>> of
>> vertices in
>> the header does not meet that indicated by the data. I did sth
>> wrong.
>>
>> Questions:
>> 1 Is this webpage still up-to-date or I shall try something
>> new to
>> flatten
>> the surface?
>> 2 Probably there are "frequently made mistakes" during my
>> manual
>> process,
>> would you please give me a hint? I my case afterwards
>> mris_flatten
>> took 2-3
>> hours.
>>
>> btw: the inflated surface is OK either checked by freeview or
>> matlab.
>>
>> best
>> Peng
>>
>>
>>
>>   ___
>>   Freesurfer mailing list
>>   Freesurfer@nmr.mgh.harvard.edu
>>   https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>   The information in this e-mail is intended only for the person to
>> whom it is
>>   addressed. If you believe this e-mail was sent to you in error and
>> the e-mail
>>   contains patient information, please contact the Partners
>> Compliance HelpLine at
>>   http://www.partners.org/complianceline . If the e-mail was sent to
>> you in error
>>   but does not contain patient information, please contact the sender
>> and properly
>>   dispose of the e-mail.
>>
>>
>>
>>
> ___
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> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addres

[Freesurfer] .w file for freeview

[peng]

Hi Freesurfers,

   I tried to overlay .w file onto a surface, and failed. I dug the
previous posts and know this file format is obsolete now. However I wish to
know in which version of freeview can I still use this file format, if
possible. It will be great if you can provide the link for it. If this is
not possible, is there a matlab tool similar to 'write_file.m' so I can
output my data in matlab to the newer format (substitution of w-file)?
   Thanks in advance.

best
Peng
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Re: [Freesurfer] .w file for freeview

[peng]

Thank you Bruce!

On Wed, Jan 6, 2016 at 8:03 PM, Bruce Fischl 
wrote:

> Hi Peng
>
> you can use read_wfile to read it into matlab, then save_mgh or MRIwrite
> to save them in .mgz format. Note that you will need to make sure that the
> vector you are writing is the correct length. The w-files can be sparse
> (that is, every vertex doesn't have to have a  value), but the .mgz files
> cannot be, so you'll need to create a vector that is nvertices in length
> (the number of vertices in the surface you are using), then set the entries
> in the vertices given to you by read_wfile to the values it gives you
>
> cheers
> Bruce
>
>
> On Tue, 29 Dec 2015, peng wrote:
>
> Hi Freesurfers,
>>I tried to overlay .w file onto a surface, and failed. I dug the
>> previous
>> posts and know this file format is obsolete now. However I wish to know in
>> which version of freeview can I still use this file format, if possible.
>> It
>> will be great if you can provide the link for it. If this is not possible,
>> is there a matlab tool similar to 'write_file.m' so I can output my data
>> in
>> matlab to the newer format (substitution of w-file)?
>>Thanks in advance.
>>
>> best
>> Peng
>>
>>
> ___
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
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> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
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Re: [Freesurfer] .w file for freeview

[peng]

Thank you Douglas!

On Wed, Jan 6, 2016 at 8:10 PM, Douglas N Greve 
wrote:

> You can also use mri_surf2surf to convert it to mgh or curv format
>
> On 01/06/2016 02:03 PM, Bruce Fischl wrote:
> > Hi Peng
> >
> > you can use read_wfile to read it into matlab, then save_mgh or
> > MRIwrite to save them in .mgz format. Note that you will need to make
> > sure that the vector you are writing is the correct length. The
> > w-files can be sparse (that is, every vertex doesn't have to have a
> > value), but the .mgz files cannot be, so you'll need to create a
> > vector that is nvertices in length (the number of vertices in the
> > surface you are using), then set the entries in the vertices given to
> > you by read_wfile to the values it gives you
> >
> > cheers
> > Bruce
> >
> >
> > On Tue, 29 Dec 2015, peng wrote:
> >
> >> Hi Freesurfers,
> >>I tried to overlay .w file onto a surface, and failed. I dug the
> >> previous
> >> posts and know this file format is obsolete now. However I wish to
> >> know in
> >> which version of freeview can I still use this file format, if
> >> possible. It
> >> will be great if you can provide the link for it. If this is not
> >> possible,
> >> is there a matlab tool similar to 'write_file.m' so I can output my
> >> data in
> >> matlab to the newer format (substitution of w-file)?
> >>Thanks in advance.
> >>
> >> best
> >> Peng
> >>
> >>
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
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>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
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> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
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[Freesurfer] freeview command line options

[peng]

Dear Freesurfer experts,

When I use Freeview GUI to show overlays on a surface, I can click on
the button "Configure", and then check the box "Enable" in the smooth
section (upper right of the pop-out window), to smooth it. Is there
any options to do similar stuff in the command line of freeview? e.g.
when I want to generate a lot of screenshots by the -ss option.
Thank you in advance!

best
Peng
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Re: [Freesurfer] freeview command line options

[peng]

Dear Ruopeng,

   Thank you for the information.

best
Peng

On Fri, Jan 27, 2017 at 4:10 PM, Ruopeng Wang
 wrote:
> Hi Peng,
>
> No, there is no command-line option for that. I will add it in future update.
>
> Best,
> Ruopeng
>
>> On Jan 27, 2017, at 9:49 AM, peng  wrote:
>>
>> Dear Freesurfer experts,
>>
>> When I use Freeview GUI to show overlays on a surface, I can click on
>> the button "Configure", and then check the box "Enable" in the smooth
>> section (upper right of the pop-out window), to smooth it. Is there
>> any options to do similar stuff in the command line of freeview? e.g.
>> when I want to generate a lot of screenshots by the -ss option.
>> Thank you in advance!
>>
>> best
>> Peng
>> ___
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>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>
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>
>
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> addressed. If you believe this e-mail was sent to you in error and the e-mail
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> at
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Re: [Freesurfer] freeview command line options

[peng]

Thanks for the advice, bruce.

On Fri, Jan 27, 2017 at 4:17 PM, Bruce Fischl
 wrote:
> probably you should just smooth the volume and save it as a new volume
> before running freeview
>
> cheers
> Bruce
> On Fri, 27 Jan 2017, Ruopeng Wang wrote:
>
>> Hi Peng,
>>
>> No, there is no command-line option for that. I will add it in future update.
>>
>> Best,
>> Ruopeng
>>
>>> On Jan 27, 2017, at 9:49 AM, peng  wrote:
>>>
>>> Dear Freesurfer experts,
>>>
>>> When I use Freeview GUI to show overlays on a surface, I can click on
>>> the button "Configure", and then check the box "Enable" in the smooth
>>> section (upper right of the pop-out window), to smooth it. Is there
>>> any options to do similar stuff in the command line of freeview? e.g.
>>> when I want to generate a lot of screenshots by the -ss option.
>>> Thank you in advance!
>>>
>>> best
>>> Peng
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>
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>>
>>
>>
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>
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Re: [Freesurfer] FS 6.0 Freeview

[peng]

Dear Ruopeng,

   I have the same problem even before the current version 6 release, and
it was "solved" by invoke freeview from the command line (term). I guess,
to start from the icon, it might use different setup files.

best
Peng

On Fri, Feb 17, 2017 at 4:41 PM, Ruopeng Wang 
wrote:

> Or would it be possible to send us the full crash report?
>
> On Feb 17, 2017, at 10:17 AM, Z K  wrote:
>
> Hi Dan. Is there an error output to the screen or terminal window? We
> will probably need that to help diagnose the issue.
>
>
>
> On 02/17/2017 05:31 AM, Daniel Carey wrote:
>
> Dear All,
>
> I've recently installed FS 6.0 on Mac (OS 10.7.5), and have been unable
> to load volumes in Freeview. When selecting 'File > Load volume', the
> dialog box appears, but when I select any T1.mgz and click Ok, Freeview
> immediately crashes.
>
> Has anyone encountered this same issue?
>
> Best wishes,
>
> Dan
>
> ---
> Dr. Daniel Carey
> Post-Doctoral Research Fellow - Statistician
> The Irish LongituDinal Study on Ageing (TILDA)
> Trinity College Dublin
> Dublin 2, Ireland.
> Email: care...@tcd.ie <mailto:care...@tcd.ie >
>
>
>
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[Freesurfer] Freeview command line option for multiple screenshots

[peng]

Dear all,

I have several different overlays on the same brain surface. When I want to
run freeview in command line and take screenshots automatically, I need to
restart freeview and load the surface for each screenshot. Is it possible
to keep the program on and only change overlays and take screenshots for
each of them? It seems possible in GUI but I don't know how to realise in
command line.
Another question is, when I have the overlay on, before taking the
screenshot, is it possible to mark a location, by e.g. a
dot/circle/square/cross/etc, the colour of the marker shall be independent
of the overlay.  I have the index  of this location in the surface
vertices.

Thank you in advance.


best
Peng
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[Freesurfer] functional data on freeview

[peng]

Dear freesurfer users,

   I have installed freesurfer and freeview. The visualization of
brain surfaces looks great. Is it possible to visualize functional
MEG/EEG source data with freeview?

What I have:
1. Source locations (Nx3)
2. Activation strength (Nx1) at these locations
3. The anatomy data from the same subject, processed by freesurfer.
4. Softwares, matlab2014b, freesurfer v5.3, MNE2.7.4

Thank you very much!

best
Peng
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Re: [Freesurfer] functional data on freeview

[peng]

Hi Bruce,

   Thank you for your help, I will also post this in the MNE group.

best
Peng

On Fri, Dec 12, 2014 at 3:20 PM, Bruce Fischl
 wrote:
> Hi Peng
>
> yes, for sure. This is what Matti Hamalainen's excellent MNE package is
> designed for. I'll cc Matti so he can chime in
>
> cheers
> Bruce
>
> On Fri, 12 Dec 2014, peng
> wrote:
>
>> Dear freesurfer users,
>>
>>   I have installed freesurfer and freeview. The visualization of
>> brain surfaces looks great. Is it possible to visualize functional
>> MEG/EEG source data with freeview?
>>
>> What I have:
>> 1. Source locations (Nx3)
>> 2. Activation strength (Nx1) at these locations
>> 3. The anatomy data from the same subject, processed by freesurfer.
>> 4. Softwares, matlab2014b, freesurfer v5.3, MNE2.7.4
>>
>> Thank you very much!
>>
>> best
>> Peng
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[Freesurfer] questions on optseq2

[peng]

hi list,

  I have two conditions, one contain 2 stimuli and the other 8. The
difference between stimuli within certain condition is vey small, and
could be omitted in further analysis if they're treated equal. Now I
have two choice:
optseq2 --ntp 160 --tr 2   --psdwin 0 14   /
--ev s11 2 8   --ev s12 2 8   --ev s13 2 8  --ev s14 2 8   /
--ev t15 2 32   /
--ev s21 2 8   --ev s22 2 8   --ev s23 2 8   --ev s24 2 8   /
--ev t25 2 32   /
--nkeep 6   --o pl1   --nsearch 1
or
optseq2 --ntp 160 --tr 2   --psdwin 0 14   /
--ev s 2 64   --ev t 2 64   /
--nkeep 6   --o pl2   --nsearch 1
Obviously, the first one would need more test runs, which in fact was
nearly 2 hours for the subjects . And the second one need only 1/4
time, but is risky. I am afraid it would induce difference between
stimuli within condition.
Do you have any suggestions on it?
Thanks a lot.

Peng
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Re: [Freesurfer] questions on optseq2

[peng]

Thank you for your advice, Daniel.
I think you may suggest the latter way I mentioned in your first piece
of advice. I have two conditions with equal trials:for
target(t),32*2(t15&t25); for standard(s),8*8(s11-14,21-24). Maybe my
expression in the first email was not clear enough. I don't care the
activation of the individual stimuli within certain conditions. I just
need to balance them to make sure "I don't care" is reasonable.
Now I am going to use the seqence generated by the first piece of
code. But when evaluate it with seqefficiency, I would merge stimuli
within conditions together. Then I would run more runs than needed,
but not as much as consider the stimuli separately.
Then I would be sure the two conditions were well randomized. The
stimuli within condition were also reasonablely randomized.

I am not sure whether I correctly understand your second  piece of
advice. But I can't change the ratio because I have to combine the
fMRI data with a finished EEG experiment with the same paradigm.

On 6/29/07, Daniel G. Wakeman <[EMAIL PROTECTED]> wrote:

Hi Peng,

I'm sure Doug and others will have very valuable advice, but why not just
keep the number of trials in the two conditions equal and separate out the
individual stimuli in the actual events (dividing to keep the number of
events per condition equal).  That way you can keep your power and if you
want to do the other analysis later you can take a look at that.  You
could of course, also fiddle with the ratios, so you use 1/2 (bottom most)
the time instead of 1/4.  I'm not sure if all of this makes sense, but
according to this I believe the command would look like the one below
(Note! I kept the ratio of trials to null the same as in your examples).

optseq2 --ntp 160 --tr 2 --psdwin 0 14 --ev s11 2 32 --ev s12 2 32 --ev 21
2 8 --ev s22 2 8 --ev s23 2 8 --ev s24 2 8 --ev s25 2 8 --ev s26 2 8 --ev
s27 2 8 --ev s28 2 8

optseq2 --ntp 160 --tr 2 --psdwin 0 14 --ev s11 2 16 --ev s12 2 16 --ev 21
2 12 --ev s22 2 12 --ev s23 2 12 --ev s24 2 12 --ev s25 2 12 --ev s26 2 12
--ev s27 2 12 --ev s28 2 12

Dan

> hi list,
>
>I have two conditions, one contain 2 stimuli and the other 8. The
> difference between stimuli within certain condition is vey small, and
> could be omitted in further analysis if they're treated equal. Now I
> have two choice:
> optseq2 --ntp 160 --tr 2   --psdwin 0 14   /
> --ev s11 2 8   --ev s12 2 8   --ev s13 2 8  --ev s14 2 8   /
> --ev t15 2 32   /
> --ev s21 2 8   --ev s22 2 8   --ev s23 2 8   --ev s24 2 8   /
> --ev t25 2 32   /
> --nkeep 6   --o pl1   --nsearch 1
> or
> optseq2 --ntp 160 --tr 2   --psdwin 0 14   /
> --ev s 2 64   --ev t 2 64   /
> --nkeep 6   --o pl2   --nsearch 1
> Obviously, the first one would need more test runs, which in fact was
> nearly 2 hours for the subjects . And the second one need only 1/4
> time, but is risky. I am afraid it would induce difference between
> stimuli within condition.
> Do you have any suggestions on it?
> Thanks a lot.
>
> Peng
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[Freesurfer] May you help me with 'recon-all' errors

[Peng Zan]

Dear freesurfer expert,

I am a student from University of Maryland, learning freesurfer for MNE
analysis recently. I have a perhaps silly problem and could not solve by
myself. The problem occurred as 'recon-all -s R2261_S0283 exited with
errors...' when I was running 'recon-all -autorecon-all -subjid
R2261_S0283'. I tried several subjects and got the same error. I am
wondering whether you can look at the 'recon-all.log' file and
'recon-all.error' file and help me figure out what the problem is and how
to solve it?

Thank you very much! Looking forward to your reply!

Sincerely,
Peng


recon-all.error
Description: Binary data


recon-all.log
Description: Binary data
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Re: [Freesurfer] May you help me with 'recon-all' errors

[Peng Zan]

Thank you! Hopefully, I can either figure it out myself or be helped by
someone.

Thanks!

Best,
Peng

On Wednesday, December 9, 2015, Bruce Fischl 
wrote:

> Hi Peng
>
> nifti should be fine as input, but definitely don't use analyze. It
> doesn't preserve the direction cosines so once you convert to it you will
> never be sure which side of the image is the left hemim and which is the
> right.
>
> I can't help with the  'can't locate MNI/Startup.pm ' error. Hopefully
> someone else can.
>
> You will need some T1-weighted image with reasonably high res as input
> htough.
>
> cheers
> Bruce
>
> On Wed, 9 Dec 2015, Peng Zan wrote:
>
> Hi Bruce,
>> Thank you for your email! These dicom files are transferred from nifti
>> files, '.nii.gz' by xmedcon, and I think for this subject(R2261_S0283),
>> they
>> are not mprage or flash scans and so far I do not have mprage or flash
>> scans
>> for this subject.
>>
>> However, I do have mprage dicom files for other subjects in .img format,
>> which freesurfer cannot read(I attached two screenshots of my folder in
>> case
>> you know by their names which files can work). Since I have most of my MRI
>> data in nifti and .img formats, it is worth the efforts to make these
>> files
>> work in freesurfer. Do the input files have to be distributed into many
>> dicom slices or they can be in one file in .nii or .dcm?
>>
>> On the other hand, I also tested the my dicom files of subject R2105 (in
>> flash scans), and here comes the errors 'can't locate MNI/Startup.pm in
>> @INC...', and the 'log' file warns the input volume axes are not
>> orthogonal.
>> (see 'recon-all.log' file attached). I think the input dicoms should not
>> have coordinates themselves, they are aligned and then assigned
>> coordinates
>> by freesurfer, am I right?
>>
>> I am sorry for my verbose problems at this very beginning of using
>> freesurfer.
>>
>> Thank you very much!
>>
>> Sincerely,
>> Peng
>>
>>
>>
>>
>>
>> On Wed, Dec 9, 2015 at 3:08 PM, Bruce Fischl 
>> wrote:
>>   Hi Peng
>>
>>   it looks like we can't read your input dicom. For example, the
>>   log says:
>>   reading from
>>
>> /Users/Peng/Documents/MNE/MNE_analysis/MRI/R2261_S0283/m000-gm_A0136_N12518
>>   _S0283_20120817_P5716_averageCBF_normalized.dcm...
>>   Starting DICOMRead2()
>>   dcmfile =
>>
>> /Users/Peng/Documents/MNE/MNE_analysis/MRI/R2261_S0283/m000-gm_A0136_N12518
>>   _S0283_20120817_P5716_averageCBF_normalized.dcm
>>   dcmdir = /Users/Peng/Documents/MNE/MNE_analysis/MRI/R2261_S0283
>>   WARNING: tag ImageNumber not found in
>>
>> /Users/Peng/Documents/MNE/MNE_analysis/MRI/R2261_S0283/m000-gm_A0136_N12518
>>   _S0283_20120817_P5716_averageCBF_normalized.dcm
>>   WARNING: tag SeriesNumber not found in
>>
>> /Users/Peng/Documents/MNE/MNE_analysis/MRI/R2261_S0283/m000-gm_A0136_N12518
>>   _S0283_20120817_P5716_averageCBF_normalized.dcm
>>   WARNING: tag image orientation not found in
>>
>> /Users/Peng/Documents/MNE/MNE_analysis/MRI/R2261_S0283/m000-gm_A0136_N12518
>>   _S0283_20120817_P5716_averageCBF_normalized.dcm
>>   Ref Series No = 0
>>   Found 5 files, checking for dicoms
>>   WARNING: tag ImageNumber not found in
>>
>> /Users/Peng/Documents/MNE/MNE_analysis/MRI/R2261_S0283/m000-gm_A0136_N12518
>>   _S0283_20120817_P5716_averageCBF_normalized.dcm
>>
>>   where did that dicom file come from? And is it supposed to be a
>>   T1-weighted volume like an mprage or FLASH scan?
>>
>>   cheers
>>   Bruce
>>
>>
>>
>>   On Wed, 9 Dec 2015, Peng Zan
>>   wrote:
>>
>>   > Dear freesurfer expert,
>>   > I am a student from University of Maryland, learning
>>   freesurfer for MNE
>>   > analysis recently. I have a perhaps silly problem and could
>>   not solve by
>>   > myself. The problem occurred as 'recon-all -s R2261_S0283
>>   exited with
>>   > errors...' when I was running 'recon-all -autorecon-all
>>   -subjid
>>   > R2261_S0283'. I tried several subjects and got the same error.
>>   I am
>>   > wondering whether you can look at the 'recon-all.log' file and
>>   > 'recon-all.error' file and help me figure out wh

[Freesurfer] Errors when testing freesurfer installation

[Peng Zan]

Dear freesurfer experts,

I am new to freesurfer and I met this problem when I was testing freesurfer
installation following the instructions on the 'Testing Freesurfer'
website. I got the problems as follows when I tested command, 'tkmedit bert
orig.mgz' on heavy data from tutorial web.

Couldn't create output file
.xdebug_tkmedit--

ERROR: FreeSurfer license file /Applications/freesurfer/.license not found.

  If you are outside the NMR-Martinos Center,

  go to http://surfer.nmr.mgh.harvard.edu to

  get a valid license file (it's free).

  If you are inside the NMR-Martinos Center,

  make sure to source the standard environment.
I have had the 'license.txt' file under FREESURFER_HOME folder, and the
freeview works fine. I also created a 'fs.license' file under the home
folder and copied the license info into it, but it still did not work. May
you give any suggestions to fix this problem?

Thank you! Looking forward to your reply!

Sincerely,
Peng
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[Freesurfer] question about recon-all autorecon2 "Automatic Topology Fixer"

[Cheng Peng]

Hi!

I am a relative beginner with freesurfer and was going through the steps listed 
on freesurfer wiki about detailed description of each steps autorecon2 covers. 
During "Automatic Topology Fixer (-fix)", the description stated that "user 
should check the orig surface in the volume to make sure that it looks 
appropriate". I am wondering how should i check and compare the orig surface 
and result since i can't find a way to open surf/?h.orig.nofix or surf/?h.orig. 

Any help or insight is appreciated!

Thanks!

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Re: [Freesurfer] recon-all error

[Cheng Peng]

Hi, Bruce:

I attached the file with an email and sent it to you an hour ago and received 
an automatic reply saying it's pending for approval due to the size of the 
email. Is there another way to upload my image or it's getting processed? I 
don't want to spam you guys since i already sent it twice and got the same 
result.

Thanks!

Cheng Peng


On Wednesday, July 23, 2014 9:39 AM, Cheng Peng  wrote:
 


Hi, Bruce,

I attached the nu.mgz file with this email, i'm at home right now and would 
upload T1.mgz later if need to. As far as i know individual recon-all runs were 
completed without error (two scans on one subject, two hours apart), really 
appreciate the help!

Cheng Peng

Maryland Neuroimaging Center


On Wednesday, July 23, 2014 9:32 AM, Bruce Fischl  
wrote:
 


Hi Cheng

do the cross-sectional runs look okay? The base? If so, does the first 
intensity normalized images look ok (the T1.mgz and the nu.mgz)? If you 
can't track it down, upload the subject and we will take a look

cheers
Bruce


On Wed, 23 
Jul 2014, Cheng Peng wrote:

> Hi, Freesurfer experts:
> 
> 
> 
> I encountered an error message while i was attempting to run a longitudinal
> study (following the instructions from
> https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing, step 2
> under workflow summary)
> 
> egister_mri: find_optimal_transform
> find_optimal_transform: nsamples 2185, passno 0, spacing 8
> GCAhistoScaleImageIntensities: could not find wm peak
> resetting wm mean[0]: 102 --> 107
> resetting gm mean[0]: 64 --> 64
> input volume #1 is the most T1-like
> using real data threshold=0.0
> skull bounding box =
 (0, 0, 0) --> (255, 255, 255)
> using (85, 85, 128) as brain centroid...
> mean wm in atlas = 107, using box (53,53,96) --> (116, 116,159) to find MRI
> wm
> WARNING: gca.c::GCAhistoScaleImageIntensities: h_mri->nbins=1, mri_peak=-1
> before smoothing, mri peak at 0
> WARNING2: gca.c::GCAhistoScaleImageIntensities: h_mri->nbins=1, mri_peak=-1
> after smoothing, mri peak at 0, scaling input intensities by inf
> 
> It appears that the skull strip step has failed as brainmask.mgz is
> completely blank. I tried to look up the error message online but found
> little help there. I would really appreciate it if someone can explain the
> problem or where to look for an explaination. I attached the recon-all error
> log with this email, i would also include nu.mgz but the last email attached
> with that was blocked due to the size of the image.
> 
> Thanks!
> 
> Best Regards,
> 
> Cheng Peng
> 
> Maryland Neuroimaging Center
> 
> 
> 
> 
> 
> 
> 
>
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[Freesurfer] FreeSurfer Registration Error

[Peng Wang]

External Email - Use Caution

Whatever I filled the form I got "Spammer. Go away!" message. Please help!
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Re: [Freesurfer] FreeSurfer Registration Error

[Peng Wang]

External Email - Use Caution

The freesurfer license.

https://surfer.nmr.mgh.harvard.edu/registration.html


On Wed, Feb 13, 2019 at 1:38 PM Hoopes, Andrew 
wrote:

> Hi, what are you trying to register for? A wiki account?
>
> Andrew
>
>
>
>
>
> *From: * on behalf of Peng Wang <
> pen...@gmail.com>
> *Reply-To: *FS Help 
> *Date: *Wednesday, February 13, 2019 at 12:54 PM
> *To: *FS Help 
> *Subject: *[Freesurfer] FreeSurfer Registration Error
>
>
>
> *External Email - Use Caution*
>
> Whatever I filled the form I got "Spammer. Go away!" message. Please help!
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[Freesurfer] License Registration Error "Spammer, go away!"

[Peng Wang]

External Email - Use Caution

Please help!

Repost with a better title.
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Re: [Freesurfer] License Registration Error "Spammer, go away!"

[Peng Wang]

External Email - Use Caution

Then it was the Firefox's built-in auto-fill triggered the spam detection.

Finally got the license file. Thanks.

On Wed, Feb 13, 2019 at 4:18 PM Hoopes, Andrew 
wrote:

> Are you using some sort of form auto-fill plugin when you're accessing the
> registration page? Our spam filter checks if a hidden parameter has been
> supplied. If there's a way for you to turn auto-fill off temporarily - I
> would try that first. Let me know how that goes.
>
> best
> Andrew
>
>
> On 2/13/19, 4:08 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf
> of Greve, Douglas N.,Ph.D."  behalf of dgr...@mgh.harvard.edu> wrote:
>
> it would be helpful if you were to tell us exactly what you were doing
> (eg, URL, which text box, etc)
>
> On 2/13/19 3:49 PM, Peng Wang wrote:
> >
> > External Email - Use Caution
> >
> > Please help!
> >
> > Repost with a better title.
> >
> > ___
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> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
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>
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[Freesurfer] Individual surface

[Alex Peng]

External Email - Use Caution

Hi FreeSurfer experts,

I am having trouble with making individual surface as template.

1. I reconstructed a macaque T1 to his individual surface and I want to
make it as my macaque template. However the vertices number of left hemi
and right hemi are different. How can I revise them to have same vertices
just like fsaverage template?

2. Since subcortical mask draw by myself, the generated medial wall regions
on the surfaces are not smooth. Is there any way that allows me to smooth
the medial wall region on surface space?

3. Currently, the generated surface have about 10k vertices on each hemi.
How can I downsample them and get the transform matrix between them because
I also want to project bold data to the downsampled surface. I have tried
mris_decimate, it only gives me a downsampled surface without transform
matrix.

Thanks for your help. Appreciate it!

X. Peng
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[Freesurfer] Error with recon-all: You are trying to re-run an existing subject with (possibly) new input data (-i).

[Peng Liu]

External Email - Use Caution

Dear all,

I am trying to run recon-all command for a subject ben. Before I perform
this command, I have exported SUBJECTS_DIR to a folder with only T1 data
for this subject ben in it. However after I entered the command "recon-all
-s ben -i T1.nii -all", this error showed up:

ERROR: You are trying to re-run an existing subject with (possibly)

 new input data (-i). If this is truly new input data, you should delete

 the subject folder and re-run, or specify a different subject name.

 If you are just continuing an analysis of an existing subject, then

 omit all -i flags.

I have tried all the suggestions listed in the error information, but none
worked.

Does anyone have any suggestion? I would really appreciated it.

Many Thanks

Peng
----
Peng Liu, PhD Candidate

Institut für Kognitive Neurologie und Demenzforschung (IKND)
Otto-von-Guericke Universität Magdeburg
Deutsches Zentrum für Neurodegenerative Erkrankungen e.V. (DZNE)

Leipziger Str. 44| Haus 64| Raum 217
39120 Magdeburg, Deutschland

Email: peng@med.ovgu.de/peng@dzne.de
Phone: +49 391 67 25074
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Re: [Freesurfer] Error with recon-all: You are trying to re-run an existing subject with (possibly) new input data (-i).

[Peng Liu]

External Email - Use Caution

Hi Andrew,

Thank you for your reply. I have tried this command you sent me

rm -rf $SUBJECTS_DIR/ben

It indeed deleted the ben folder under the subject directory, but when I
try to run recon-all for this participant under another name, it still
responds with the same error.

I have also tried the same data in another laptop. Also showed up the
error. Would you say it might be something wrong with the data itself?
(Although I am quite certain this is the raw T1 data which has never been
performed any analysis).

Many Thanks

Peng


Peng Liu, PhD Candidate

Institut für Kognitive Neurologie und Demenzforschung (IKND)
Otto-von-Guericke Universität Magdeburg
Deutsches Zentrum für Neurodegenerative Erkrankungen e.V. (DZNE)

Leipziger Str. 44| Haus 64| Raum 217
39120 Magdeburg, Deutschland

Email: peng@med.ovgu.de/peng@dzne.de
Phone: +49 391 67 25074


On Fri, 20 Mar 2020 at 14:33, Hoopes, Andrew 
wrote:

> Hi Peng,
>
>
>
> Are you sure you’re deleting the subject folder from within the
> SUBJECTS_DIR?
>
>
>
> rm -rf $SUBJECTS_DIR/ben
>
>
>
> Should clear the issue.
>
>
>
> best
>
> Andrew
>
>
>
>
>
> *From: * on behalf of Peng Liu <
> claudialiu1...@gmail.com>
> *Reply-To: *FS Help 
> *Date: *Friday, March 20, 2020 at 6:39 AM
> *To: *FS Help 
> *Subject: *[Freesurfer] Error with recon-all: You are trying to re-run an
> existing subject with (possibly) new input data (-i).
>
>
>
> *External Email - Use Caution*
>
> Dear all,
>
>
>
> I am trying to run recon-all command for a subject ben. Before I perform
> this command, I have exported SUBJECTS_DIR to a folder with only T1 data
> for this subject ben in it. However after I entered the command "recon-all
> -s ben -i T1.nii -all", this error showed up:
>
>
>
> ERROR: You are trying to re-run an existing subject with (possibly)
>
>  new input data (-i). If this is truly new input data, you should delete
>
>  the subject folder and re-run, or specify a different subject name.
>
>  If you are just continuing an analysis of an existing subject, then
>
>  omit all -i flags.
>
>
>
> I have tried all the suggestions listed in the error information, but none
> worked.
>
>
>
> Does anyone have any suggestion? I would really appreciated it.
>
>
>
> Many Thanks
>
>
>
> Peng
>
> 
>
> Peng Liu, PhD Candidate
>
>
>
> Institut für Kognitive Neurologie und Demenzforschung (IKND)
>
> Otto-von-Guericke Universität Magdeburg
>
> Deutsches Zentrum für Neurodegenerative Erkrankungen e.V. (DZNE)
>
>
>
> Leipziger Str. 44| Haus 64| Raum 217
>
> 39120 Magdeburg, Deutschland
>
>
>
> Email: peng@med.ovgu.de/peng@dzne.de
>
> Phone: +49 391 67 25074
> ___
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Re: [Freesurfer] Error with recon-all: You are trying to re-run an existing subject with (possibly) new input data (-i).

[Peng Liu]

External Email - Use Caution

Hello Douglas,

If I do ls $SUBJECTS_DIR/ben, the T1 image will show up as predicted.

However if I tried to recon-all, the error will pop up.

Many Thanks


Peng Liu, PhD Candidate

Institut für Kognitive Neurologie und Demenzforschung (IKND)
Otto-von-Guericke Universität Magdeburg
Deutsches Zentrum für Neurodegenerative Erkrankungen e.V. (DZNE)

Leipziger Str. 44| Haus 64| Raum 217
39120 Magdeburg, Deutschland

Email: peng@med.ovgu.de/peng@dzne.de
Phone: +49 391 67 25074


On Fri, 20 Mar 2020 at 15:54, Douglas N. Greve 
wrote:

> What is your SUBJECTS_DIR set to? What do you get if you
> ls $SUBJECTS_DIR/ben
>
> On 3/20/2020 9:48 AM, Peng Liu wrote:
>
> External Email - Use Caution
> Hi Andrew,
>
> Thank you for your reply. I have tried this command you sent me
>
> rm -rf $SUBJECTS_DIR/ben
>
> It indeed deleted the ben folder under the subject directory, but when I
> try to run recon-all for this participant under another name, it still
> responds with the same error.
>
> I have also tried the same data in another laptop. Also showed up the
> error. Would you say it might be something wrong with the data itself?
> (Although I am quite certain this is the raw T1 data which has never been
> performed any analysis).
>
> Many Thanks
>
> Peng
> 
>
> Peng Liu, PhD Candidate
>
> Institut für Kognitive Neurologie und Demenzforschung (IKND)
> Otto-von-Guericke Universität Magdeburg
> Deutsches Zentrum für Neurodegenerative Erkrankungen e.V. (DZNE)
>
> Leipziger Str. 44| Haus 64| Raum 217
> 39120 Magdeburg, Deutschland
>
> Email: peng@med.ovgu.de/peng@dzne.de
> Phone: +49 391 67 25074
>
>
> On Fri, 20 Mar 2020 at 14:33, Hoopes, Andrew 
> wrote:
>
>> Hi Peng,
>>
>>
>>
>> Are you sure you’re deleting the subject folder from within the
>> SUBJECTS_DIR?
>>
>>
>>
>> rm -rf $SUBJECTS_DIR/ben
>>
>>
>>
>> Should clear the issue.
>>
>>
>>
>> best
>>
>> Andrew
>>
>>
>>
>>
>>
>> *From: * on behalf of Peng Liu <
>> claudialiu1...@gmail.com>
>> *Reply-To: *FS Help 
>> *Date: *Friday, March 20, 2020 at 6:39 AM
>> *To: *FS Help 
>> *Subject: *[Freesurfer] Error with recon-all: You are trying to re-run
>> an existing subject with (possibly) new input data (-i).
>>
>>
>>
>> *External Email - Use Caution*
>>
>> Dear all,
>>
>>
>>
>> I am trying to run recon-all command for a subject ben. Before I perform
>> this command, I have exported SUBJECTS_DIR to a folder with only T1 data
>> for this subject ben in it. However after I entered the command "recon-all
>> -s ben -i T1.nii -all", this error showed up:
>>
>>
>>
>> ERROR: You are trying to re-run an existing subject with (possibly)
>>
>>  new input data (-i). If this is truly new input data, you should delete
>>
>>  the subject folder and re-run, or specify a different subject name.
>>
>>  If you are just continuing an analysis of an existing subject, then
>>
>>  omit all -i flags.
>>
>>
>>
>> I have tried all the suggestions listed in the error information, but
>> none worked.
>>
>>
>>
>> Does anyone have any suggestion? I would really appreciated it.
>>
>>
>>
>> Many Thanks
>>
>>
>>
>> Peng
>>
>> 
>>
>> Peng Liu, PhD Candidate
>>
>>
>>
>> Institut für Kognitive Neurologie und Demenzforschung (IKND)
>>
>> Otto-von-Guericke Universität Magdeburg
>>
>> Deutsches Zentrum für Neurodegenerative Erkrankungen e.V. (DZNE)
>>
>>
>>
>> Leipziger Str. 44| Haus 64| Raum 217
>>
>> 39120 Magdeburg, Deutschland
>>
>>
>>
>> Email: peng@med.ovgu.de/peng@dzne.de
>>
>> Phone: +49 391 67 25074
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
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>
>
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[Freesurfer] (no subject)

[Peng Liu]

External Email - Use Caution

Dear Freesurfer experts,

I am trying to customize a colour map of my own, with five colours and
scale from -12.5 to 12.5, since when using Heat (with default options), the
scale is correct but it is shown in only four colours.

However after I created the .lut file (attached below), when loading it
into freeview, the colour scale is from 0 to 6.

[image: image.png]

Does this mean I should also include scale information in the .lut file?

Any help would be much appreciated.

Peng Liu


Map.lut
Description: Binary data
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[Freesurfer] Customizing colour map

[Peng Liu]

External Email - Use Caution

Dear Freesurfer experts,

I am trying to customize a colour map of my own, with five colours and
scale from -12.5 to 12.5, since when using Heat (with default options), the
scale is correct but it is shown in only four colours.

However after I created the .lut file (attached below), when loading it
into freeview, the colour scale is from 0 to 6.

[image: image.png]

Does this mean I should also include scale information in the .lut file?

Any help would be much appreciated.

Peng Liu


Map.lut
Description: Binary data
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Re: [Freesurfer] (no subject)

[Peng Liu]

External Email - Use Caution

Hi Ruopeng,

Thank you for your reply.

I have also tried NIH and JET, but with negative scale, the entire image
will turn into one same color as if there is some error.

Meanwhile the reason of me trying to create .lut map is because I want five
colours and five colours only...

Is there any specific reason to not display negative scales with look up
table? Will it cause any error or jeopardize the results displayed?

Many Thanks

Peng


On Mon, 6 Apr 2020 at 16:13, Ruopeng Wang 
wrote:

> Hi Peng,
>
> Your lookup table only contains indices between 0 to 6. In any case I
> would not use look up table to display negative scales. Have you tried any
> other color maps like JET or NIH which has more colors?
>
> Best,
> Ruopeng
>
> On Apr 6, 2020, at 6:30 AM, Peng Liu  wrote:
>
> External Email - Use Caution
>
> Dear Freesurfer experts,
>
> I am trying to customize a colour map of my own, with five colours and
> scale from -12.5 to 12.5, since when using Heat (with default options), the
> scale is correct but it is shown in only four colours.
>
> However after I created the .lut file (attached below), when loading it
> into freeview, the colour scale is from 0 to 6.
>
> 
>
> Does this mean I should also include scale information in the .lut file?
>
> Any help would be much appreciated.
>
> Peng Liu
> ___
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>
>
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Re: [Freesurfer] (no subject)

[Peng Liu]

External Email - Use Caution

Thank you so much. I shall modify my other scripts then.

Peng


On Mon, 6 Apr 2020 at 16:59, Ruopeng Wang 
wrote:

> I don’t think look up table works with negative indices. It was mainly
> designed for label volumes.
>
> Ruopeng
>
> On Apr 6, 2020, at 10:35 AM, Peng Liu  wrote:
>
> External Email - Use Caution
>
> Hi Ruopeng,
>
> Thank you for your reply.
>
> I have also tried NIH and JET, but with negative scale, the entire image
> will turn into one same color as if there is some error.
>
> Meanwhile the reason of me trying to create .lut map is because I want
> five colours and five colours only...
>
> Is there any specific reason to not display negative scales with look up
> table? Will it cause any error or jeopardize the results displayed?
>
> Many Thanks
>
> Peng
>
>
> On Mon, 6 Apr 2020 at 16:13, Ruopeng Wang 
> wrote:
>
>> Hi Peng,
>>
>> Your lookup table only contains indices between 0 to 6. In any case I
>> would not use look up table to display negative scales. Have you tried any
>> other color maps like JET or NIH which has more colors?
>>
>> Best,
>> Ruopeng
>>
>> On Apr 6, 2020, at 6:30 AM, Peng Liu  wrote:
>>
>> External Email - Use Caution
>>
>> Dear Freesurfer experts,
>>
>> I am trying to customize a colour map of my own, with five colours and
>> scale from -12.5 to 12.5, since when using Heat (with default options), the
>> scale is correct but it is shown in only four colours.
>>
>> However after I created the .lut file (attached below), when loading it
>> into freeview, the colour scale is from 0 to 6.
>>
>> 
>>
>> Does this mean I should also include scale information in the .lut file?
>>
>> Any help would be much appreciated.
>>
>> Peng Liu
>> ___
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>>
>>
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>
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>
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[Freesurfer] Recon-all Talairach failed error

[Peng Liu]

External Email - Use Caution

Dear Freesurfer experts,

I am trying to run recon-all for a new subject, however I came across with
this error 'Talairach failed'. The error log is as following:















*talairach done\n cp transforms/talairach.auto.xfm transforms/talairach.xfm
\n##@# Talairach Failure
Detection Thu May 14 15:11:47 CEST
2020/Users/pliu/Documents/DataAnalysis0512/subjects/Pilot03/mri\n
talairach_afd -T 0.005 -xfm transforms/talairach.xfm \nERROR:
talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED***
(p=0.0153, pval=0. < threshold=0.0050)\nManual Talairach alignment may
be necessary, orinclude the -notal-check flag to skip this test,making sure
the -notal-check flag follows -allor -autorecon1 in the command
string.See:\nhttp://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach
<http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach>\nERROR:
Talairach failed!\n*

I have read online that I might need to perform a rough coregistration for
the input image before running recon-all. But I am a bit lost by which
image should it be registered to... Would 'mni305.cor.mgz' be okay as
reference image?

Any help would be much appreciated.

Kindly Regards

Peng Liu

[image: Otto-von-Guericke University Magdeburg]

Peng Liu, PhD Candidate

Institut für Kognitive Neurologie und Demenzforschung (IKND)
Otto-von-Guericke Universität Magdeburg
Deutsches Zentrum für Neurodegenerative Erkrankungen e.V. (DZNE)

Leipziger Str. 44| Haus 64| Raum 217
39120 Magdeburg, Deutschland

Email: peng@med.ovgu.de/peng@dzne.de
Phone: +49 391 67 25074
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[Freesurfer] Brodmann area labels

[Peng Liu]

External Email - Use Caution

Dear Freesurfer experts,

I was trying to perform some ROI analysis with results obtained from
recon-all. However I noticed that after recon-all, the labels created were
like 'lh.BA3b*_exvivo*.label', whereas the labels I would want to create
are like 'lh.BA3b.label'.

I have tried mri_annotation2label command, but the results I got were not
as wanted either.

Does anyone know how to create labels like 'lh.BA3b.label'?

Any help would be appreciated a lot!

Many Thanks

PL

[image: Otto-von-Guericke University Magdeburg]

Peng Liu, PhD Candidate

Institut für Kognitive Neurologie und Demenzforschung (IKND)
Otto-von-Guericke Universität Magdeburg
Deutsches Zentrum für Neurodegenerative Erkrankungen e.V. (DZNE)

Leipziger Str. 44| Haus 64| Raum 217
39120 Magdeburg, Deutschland

Email: peng@med.ovgu.de/peng@dzne.de
Phone: +49 391 67 25074
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Re: [Freesurfer] Brodmann area labels

[Peng Liu]

External Email - Use Caution

Hi Douglas,

Previously, after I ran recon-all, I would get multiple labels for the same
brain area. For example, for BA3b, I have BA3b.label, BA3b.hmap.label and
BA3b.thresh.label for each hemisphere.

However this time I only have BA3b_exvivo.label, I wonder how would I get
other labels, which command should I run?

Many Thanks

PL


On Wed, 24 Jun 2020 at 16:09, Douglas N. Greve 
wrote:

> I'm not sure what you mean by "like lh.BA3b.label". Are you just talking
> about the file name or the actual label?
>
> On 6/24/2020 7:37 AM, Peng Liu wrote:
>
> External Email - Use Caution
> Dear Freesurfer experts,
>
> I was trying to perform some ROI analysis with results obtained from
> recon-all. However I noticed that after recon-all, the labels created were
> like 'lh.BA3b*_exvivo*.label', whereas the labels I would want to create
> are like 'lh.BA3b.label'.
>
> I have tried mri_annotation2label command, but the results I got were not
> as wanted either.
>
> Does anyone know how to create labels like 'lh.BA3b.label'?
>
> Any help would be appreciated a lot!
>
> Many Thanks
>
> PL
> 
> [image: Otto-von-Guericke University Magdeburg]
>
> Peng Liu, PhD Candidate
>
> Institut für Kognitive Neurologie und Demenzforschung (IKND)
> Otto-von-Guericke Universität Magdeburg
> Deutsches Zentrum für Neurodegenerative Erkrankungen e.V. (DZNE)
>
> Leipziger Str. 44| Haus 64| Raum 217
> 39120 Magdeburg, Deutschland
>
> Email: peng@med.ovgu.de/peng@dzne.de
> Phone: +49 391 67 25074
>
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>
>
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Re: [Freesurfer] Brodmann area labels

[Peng Liu]

External Email - Use Caution

Hi Bruce,

I have tried this label, but it seems not working as it should be. That is
why I wanted to create labels like before.

Thank you so much!

PL

On Wed, 24 Jun 2020 at 16:58, Fischl, Bruce  wrote:

> Hi Peng
>
>
>
> I think 'lh.BA3b*_exvivo*.label' is the label you want. The _exvivo just
> means that the data that went into the prediction was acquired on ex vivo
> brains.
>
> Cheers
>
> Bruce
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Peng Liu
> *Sent:* Wednesday, June 24, 2020 7:38 AM
> *To:* Freesurfer support list 
> *Subject:* [Freesurfer] Brodmann area labels
>
>
>
> *External Email - Use Caution*
>
> Dear Freesurfer experts,
>
>
>
> I was trying to perform some ROI analysis with results obtained from
> recon-all. However I noticed that after recon-all, the labels created were
> like 'lh.BA3b*_exvivo*.label', whereas the labels I would want to create
> are like 'lh.BA3b.label'.
>
>
>
> I have tried mri_annotation2label command, but the results I got were not
> as wanted either.
>
>
>
> Does anyone know how to create labels like 'lh.BA3b.label'?
>
>
>
> Any help would be appreciated a lot!
>
>
>
> Many Thanks
>
>
>
> PL
>
> 
>
> [image: Otto-von-Guericke University Magdeburg]
>
>
>
> Peng Liu, PhD Candidate
>
>
>
> Institut für Kognitive Neurologie und Demenzforschung (IKND)
>
> Otto-von-Guericke Universität Magdeburg
>
> Deutsches Zentrum für Neurodegenerative Erkrankungen e.V. (DZNE)
>
>
>
> Leipziger Str. 44| Haus 64| Raum 217
>
> 39120 Magdeburg, Deutschland
>
>
>
> Email: peng@med.ovgu.de/peng@dzne.de
>
> Phone: +49 391 67 25074
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
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Re: [Freesurfer] Brodmann area labels

[Peng Liu]

External Email - Use Caution

I usually convert BA3b.label to a nifti mask with SPM to perform ROI
analysis. But with exvivo label, the mask seems not working.

Many Thanks

PL

On Thu, 25 Jun 2020 at 16:24, Fischl, Bruce  wrote:

> Can you elaborate? What do you mean it is not working as it should be?
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Peng Liu
> *Sent:* Thursday, June 25, 2020 7:23 AM
> *To:* Freesurfer support list 
> *Subject:* Re: [Freesurfer] Brodmann area labels
>
>
>
> *External Email - Use Caution*
>
> Hi Bruce,
>
>
>
> I have tried this label, but it seems not working as it should be. That is
> why I wanted to create labels like before.
>
>
>
> Thank you so much!
>
>
>
> PL
>
>
>
> On Wed, 24 Jun 2020 at 16:58, Fischl, Bruce 
> wrote:
>
> Hi Peng
>
>
>
> I think 'lh.BA3b*_exvivo*.label' is the label you want. The _exvivo just
> means that the data that went into the prediction was acquired on ex vivo
> brains.
>
> Cheers
>
> Bruce
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Peng Liu
> *Sent:* Wednesday, June 24, 2020 7:38 AM
> *To:* Freesurfer support list 
> *Subject:* [Freesurfer] Brodmann area labels
>
>
>
> *External Email - Use Caution*
>
> Dear Freesurfer experts,
>
>
>
> I was trying to perform some ROI analysis with results obtained from
> recon-all. However I noticed that after recon-all, the labels created were
> like 'lh.BA3b*_exvivo*.label', whereas the labels I would want to create
> are like 'lh.BA3b.label'.
>
>
>
> I have tried mri_annotation2label command, but the results I got were not
> as wanted either.
>
>
>
> Does anyone know how to create labels like 'lh.BA3b.label'?
>
>
>
> Any help would be appreciated a lot!
>
>
>
> Many Thanks
>
>
>
> PL
>
> 
>
> [image: Otto-von-Guericke University Magdeburg]
>
>
>
> Peng Liu, PhD Candidate
>
>
>
> Institut für Kognitive Neurologie und Demenzforschung (IKND)
>
> Otto-von-Guericke Universität Magdeburg
>
> Deutsches Zentrum für Neurodegenerative Erkrankungen e.V. (DZNE)
>
>
>
> Leipziger Str. 44| Haus 64| Raum 217
>
> 39120 Magdeburg, Deutschland
>
>
>
> Email: peng@med.ovgu.de/peng@dzne.de
>
> Phone: +49 391 67 25074
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
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Re: [Freesurfer] Brodmann area labels

[Peng Liu]

External Email - Use Caution

Not exactly. I can successfully create a nifti mask with this
exvivo label, and the brain area it highlighted is correct
from observation. But when I try to employ this mask to ROI analysis. The
results I got are exactly the same, with and without this mask.

That is why I said it seems not working.

If exvivo label is the same label as I used before, I will further look
into the script and parameter setups.

Thank you for all your help

PL

On Thu, 25 Jun 2020 at 19:20, Tim Schäfer  wrote:

> External Email - Use Caution
>
> What do you mean with 'not working'? Is an incorrect area highlighted on
> the brain? Does some command you are using respond with an error message?
>
> Tim
>
> > On June 25, 2020 at 5:33 PM Peng Liu  wrote:
> >
> >
> > External Email - Use Caution
> >
> > I usually convert BA3b.label to a nifti mask with SPM to perform ROI
> > analysis. But with exvivo label, the mask seems not working.
> >
> > Many Thanks
> >
> > PL
> >
> > On Thu, 25 Jun 2020 at 16:24, Fischl, Bruce 
> wrote:
> >
> > > Can you elaborate? What do you mean it is not working as it should be?
> > >
> > >
> > >
> > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> > > freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Peng Liu
> > > *Sent:* Thursday, June 25, 2020 7:23 AM
> > > *To:* Freesurfer support list 
> > > *Subject:* Re: [Freesurfer] Brodmann area labels
> > >
> > >
> > >
> > > *External Email - Use Caution*
> > >
> > > Hi Bruce,
> > >
> > >
> > >
> > > I have tried this label, but it seems not working as it should be.
> That is
> > > why I wanted to create labels like before.
> > >
> > >
> > >
> > > Thank you so much!
> > >
> > >
> > >
> > > PL
> > >
> > >
> > >
> > > On Wed, 24 Jun 2020 at 16:58, Fischl, Bruce 
> > > wrote:
> > >
> > > Hi Peng
> > >
> > >
> > >
> > > I think 'lh.BA3b*_exvivo*.label' is the label you want. The _exvivo
> just
> > > means that the data that went into the prediction was acquired on ex
> vivo
> > > brains.
> > >
> > > Cheers
> > >
> > > Bruce
> > >
> > >
> > >
> > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> > > freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Peng Liu
> > > *Sent:* Wednesday, June 24, 2020 7:38 AM
> > > *To:* Freesurfer support list 
> > > *Subject:* [Freesurfer] Brodmann area labels
> > >
> > >
> > >
> > > *External Email - Use Caution*
> > >
> > > Dear Freesurfer experts,
> > >
> > >
> > >
> > > I was trying to perform some ROI analysis with results obtained from
> > > recon-all. However I noticed that after recon-all, the labels created
> were
> > > like 'lh.BA3b*_exvivo*.label', whereas the labels I would want to
> create
> > > are like 'lh.BA3b.label'.
> > >
> > >
> > >
> > > I have tried mri_annotation2label command, but the results I got were
> not
> > > as wanted either.
> > >
> > >
> > >
> > > Does anyone know how to create labels like 'lh.BA3b.label'?
> > >
> > >
> > >
> > > Any help would be appreciated a lot!
> > >
> > >
> > >
> > > Many Thanks
> > >
> > >
> > >
> > > PL
> > >
> > > 
> > >
> > > [image: Otto-von-Guericke University Magdeburg]
> > >
> > >
> > >
> > > Peng Liu, PhD Candidate
> > >
> > >
> > >
> > > Institut für Kognitive Neurologie und Demenzforschung (IKND)
> > >
> > > Otto-von-Guericke Universität Magdeburg
> > >
> > > Deutsches Zentrum für Neurodegenerative Erkrankungen e.V. (DZNE)
> > >
> > >
> > >
> > > Leipziger Str. 44| Haus 64| Raum 217
> > >
> > > 39120 Magdeburg, Deutschland
> > >
> > >
> > >
> > > Email: peng@med.ovgu.de/peng@dzne.de
> > >
> > > Phone: +49 391 67 25074
> > >
> > > ___
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > >
> > > ___
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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[Freesurfer] pass code for FS_7_2_0_Ubuntu_18_04_06.ova.7z

[Peng, Shichun]

External Email - Use Caution

Could you please send me the pass code to unzip the file?

Thanks,
Shichun

The information contained in this electronic e-mail transmission and any 
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 .
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continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] [EXTERNAL] Re: pass code for FS_7_2_0_Ubuntu_18_04_06.ova.7z

[Peng, Shichun]

External Email - Use Caution

For some reasons I haven’t received the email yet.
Could you please send the pass code to me again?

Thanks,
Shichun

From: fsbuild [mailto:fsbu...@contbay.com]
Sent: Tuesday, April 26, 2022 8:39 AM
To: freesurfer@nmr.mgh.harvard.edu
Cc: Peng, Shichun 
Subject: [EXTERNAL] Re: [Freesurfer] pass code for 
FS_7_2_0_Ubuntu_18_04_06.ova.7z


External Email. Do not click links or open attachments unless you trust the 
sender and content. Report suspicious emails using Report Phishing button or 
forward email to ph...@northwell.edu<mailto:ph...@northwell.edu>

Sending the info to your email shortly..

- R.


On Apr 23, 2022, at 20:56, Peng, Shichun 
mailto:sp...@northwell.edu>> wrote:

External Email - Use Caution
Could you please send me the pass code to unzip the file?

Thanks,
Shichun
The information contained in this electronic e-mail transmission and any 
attachments are intended only for the use of the individual or entity to whom 
or to which it is addressed, and may contain information that is privileged, 
confidential and exempt from disclosure under applicable law. If the reader of 
this communication is not the intended recipient, or the employee or agent 
responsible for delivering this communication to the intended recipient, you 
are hereby notified that any dissemination, distribution, copying or disclosure 
of this communication and any attachment is strictly prohibited. If you have 
received this transmission in error, please notify the sender immediately by 
telephone and electronic mail, and delete the original communication and any 
attachment from any computer, server or other electronic recording or storage 
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Please note that this e-mail is not secure (encrypted).  If you do not wish to 
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